Of the two, San Pedro. Belize City has a kind of Graham Greeneish appeal for some, but other than several good restaurants, a large casino, and a few old colonial buildings, it doesn't have much for the typical visitor. Some areas of the city have a high crime rate, and even in the safe areas it is not a good idea to wander around at night.
If you want to visit the port city or other parts of the mainland, you can do so on a day trip by ferry or air.
Mayan Princess is a convenient, pleasant small condotel. I stayed there a few weeks ago. It's not one of the fanciest condos on the island (for something more upscale, consider Banana Beach or Villas at Banyan Bay), and it doesn't have a pool, but the rates are usually very attractive, and I like being on the water right in the middle of things in town.
Belize First Magazine http://www.turq.com/belizefirst/